Nature Search

Regulatory element detection using correlation with expression

Harmen J. Bussemaker
Hao Li
Eric D. Siggia
Research01 Feb 2001
Nature Genetics

Volume: 27, P: 167-171
Identification of genes expressed in C. elegans touch receptor neurons

Yun Zhang
Charles Ma
Martin Chalfie
Research18 Jul 2002
Nature

Volume: 418, P: 331-335
In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module

Hox proteins are expressed in partially overlapping regions to inform development along the embryo’s head-tail axis. Here the authors analyse a cis regulatory module directly regulated by seven different Drosophila Hox proteins to uncover how different Hox class proteins differentially control its expression.

Carlos Sánchez-Higueras
Chaitanya Rastogi
James C.-G. Hombría
ResearchOpen Access09 Aug 2019
Nature Communications

Volume: 10, P: 1-13
High-throughput identification of human SNPs affecting regulatory element activity

Application of SuRE reporter technology to survey the effect of 5.9 million SNPs in the human genome on enhancer and promoter activity identifies over 30,000 SNPs that alter the activity of putative regulatory elements.

Joris van Arensbergen
Ludo Pagie
Bas van Steensel
Research28 Jun 2019
Nature Genetics

Volume: 51, P: 1160-1169
Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning

Protein–ligand binding affinity is predicted quantitatively from sequencing data.

H. Tomas Rube
Chaitanya Rastogi
Harmen J. Bussemaker
ResearchOpen Access23 May 2022
Nature Biotechnology

Volume: 40, P: 1520-1527
Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors

Feng et al. compare the genome-wide binding and activity of two Drosophila Hox transcription factors that determine the identities of different fly legs. For binding events that are Hox specific, two cofactors, Exd and Dll, are used to achieve specificity in non-overlapping leg domains.

Siqian Feng
Chaitanya Rastogi
Richard S. Mann
ResearchOpen Access01 Jul 2022
Nature Communications

Volume: 13, P: 1-19
Genome-wide mapping of autonomous promoter activity in human cells

The intrinsic strength of promoter sequences in driving transcription is measured across the human genome.

Joris van Arensbergen
Vincent D FitzPatrick
Bas van Steensel
Research26 Dec 2016
Nature Biotechnology

Volume: 35, P: 145-153
Evaluation of methods for modeling transcription factor sequence specificity

The most comprehensive analysis to date of models of transcription-factor binding specificity reveals the best methods for predicting in vivo binding from in vitro data.

Matthew T Weirauch
Atina Cote
Timothy R Hughes
Research27 Jan 2013
Nature Biotechnology

Volume: 31, P: 126-134

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Regulatory element detection using correlation with expression

Identification of genes expressed in C. elegans touch receptor neurons

In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module

High-throughput identification of human SNPs affecting regulatory element activity

Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors

Genome-wide mapping of autonomous promoter activity in human cells

Evaluation of methods for modeling transcription factor sequence specificity

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